Annotations: 4M5D

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Nrap_D1-like	8044916	4004203	SCOP2 (2022-06-29)
A	SCOP2 Family	Nrap_D4-like	8046928	4005373	SCOP2 (2022-06-29)
A	SCOP2 Family	Nrap_D2-like	8046926	4005371	SCOP2 (2022-06-29)
A	SCOP2 Family	Nrap_D5-like	8046931	4005375	SCOP2 (2022-06-29)
A	SCOP2 Family	Nrap_D3-like	8046927	4005372	SCOP2 (2022-06-29)
A	SCOP2 Family	Nrap_D6-like	8046932	4005376	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotidyltransferase-like	8053725	3000129	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotidyltransferase-like	8053726	3000129	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PAP/OAS1 substrate-binding domain-like	8053727	3000941	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PAP/OAS1 substrate-binding domain-like	8053728	3000941	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PAP/Archaeal CCA-adding enzyme C-terminal domain-like	8053729	3001147	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PAP/Archaeal CCA-adding enzyme C-terminal domain-like	8053730	3001147	SCOP2 (2022-06-29)
B	SCOP2 Family	RRP7 N-terminal domain-like	8053723	4007617	SCOP2 (2022-06-29)
B	SCOP2 Family	RRP7 C-terminal domain-like	8048121	4005969	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RNA-binding domain RBD	8053724	3000110	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RRP7 C-terminal domain-like	8053722	3002219	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Nrap_D2	e4m5dA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: Nrap_D2	ECOD (1.6)
A	Nrap_D5	e4m5dA5	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: Nrap_D5	ECOD (1.6)
A	Nrap_D3	e4m5dA3	A: a+b two layers	X: Alpha-beta plaits	H: PAP/Archaeal CCA-adding enzyme, C-terminal domain (From Topology)	T: PAP/Archaeal CCA-adding enzyme, C-terminal domain	F: Nrap_D3	ECOD (1.6)
A	Nrap_D6	e4m5dA6	A: a+b two layers	X: Alpha-beta plaits	H: PAP/Archaeal CCA-adding enzyme, C-terminal domain (From Topology)	T: PAP/Archaeal CCA-adding enzyme, C-terminal domain	F: Nrap_D6	ECOD (1.6)
A	Nrap	e4m5dA1	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: Nrap	ECOD (1.6)
A	Nrap_D4	e4m5dA4	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: Nrap_D4	ECOD (1.6)
B	KOG4008	e4m5dB1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: KOG4008	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1410.10	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain		CATH (4.3.0)
A	3.30.70.3020	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.70.3030	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	6.10.250.2760	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03813	Nrap protein domain 1 (Nrap)	Nrap protein domain 1	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1]. This domain has a nucleotidyltransferase structure.	Domain
A	PF17403	Nrap protein PAP/OAS-like domain (Nrap_D2)	Nrap protein PAP/OAS-like domain	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].	Domain
A	PF17406	Nrap protein PAP/OAS1-like domain 5 (Nrap_D5)	Nrap protein PAP/OAS1-like domain 5	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].	Domain
A	PF17407	Nrap protein domain 6 (Nrap_D6)	Nrap protein domain 6	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].	Domain
A	PF17404	Nrap protein domain 3 (Nrap_D3)	Nrap protein domain 3	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].	Domain
A	PF17405	Nrap protein nucleotidyltransferase domain 4 (Nrap_D4)	Nrap protein nucleotidyltransferase domain 4	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...	Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].	Domain
B	PF17799	Rrp7 RRM-like N-terminal domain (RRM_Rrp7)	Rrp7 RRM-like N-terminal domain	This domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein. It has an RRM-like fold with a circular permutation [1].	Domain
B	PF12923	Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain (RRP7)	Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain	RRP7 is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly [1]. It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	U3 small nucleolar RNA-associated protein 22	RNA binding binding organic cyclic compound binding nucleic acid binding	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process cellular localization RNA transport nitrogen compound transport nucleocytoplasmic transport transport nuclear transport organic substance transport nucleic acid transport intracellular transport tRNA export from nucleus establishment of localization RNA export from nucleus localization tRNA transport establishment of RNA localization establishment of localization in cell macromolecule localization RNA localization nuclear export nucleobase-containing compound transport regulation of ribosomal protein gene transcription by RNA polymerase II regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis RNA processing nucleic acid catabolic process organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribosome assembly maturation of SSU-rRNA	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex preribosome nuclear protein-containing complex 90S preribosome ribonucleoprotein complex UTP-C complex CURI complex small-subunit processome nucleoplasm
B	Ribosomal RNA-processing protein 7	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process regulation of ribosomal protein gene transcription by RNA polymerase II regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis RNA processing nucleic acid catabolic process organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribosome assembly maturation of SSU-rRNA	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex preribosome nuclear protein-containing complex 90S preribosome ribonucleoprotein complex UTP-C complex CURI complex small-subunit processome nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR035367	Nrap protein, domain 2	Domain
A	IPR035368	Nrap protein, domain 3	Domain
A	IPR035370	Nrap protein, domain 5	Domain
A	IPR005554	NOL6/Upt22	Family
A	IPR035369	Nrap protein, domain 4	Domain
A	IPR035082	Nrap protein domain 1	Domain
A	IPR035371	Nrap protein, domain 6	Domain
B	IPR040446	Ribosomal RNA-processing protein 7	Family
B	IPR040447	Rrp7, RRM-like N-terminal domain	Domain
B	IPR024326	Ribosomal RNA-processing protein 7, C-terminal domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.